Search Results for "reaction" - Page 2
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Showing 102 open source projects for "reaction"
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With the world of work changed forever, it’s essential to manage your workplace and assets together to effectively create a high-performing environment. The Eptura experience combines the power of workplace management software with asset management, enabling you to effectively operate your building and facilitate hybrid work.
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Regroup Mass Notification empowers better mass communication that keeps people safe and informed at all times. The company’s award-winning, cloud-based mass communication platform is what clients across North America and around the globe rely on to send both emergency and day-to-day communications to millions of people. By enabling one-click messaging to mobile devices, landlines, social media, email, websites, and more, Regroup Mass Notification helps organizations keep people safe, strengthen operational resilience, mitigate risk, and thrive in an increasingly unpredictable world.
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. -
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
... be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. We distinguish four groups of models: (1) flux balance models that only define reaction kinetics for substrate uptake and by-product excretion, (2) kinetic models without and (3) kinetic models with regulation on the metabolic and/or genetic level, and (4) resource allocation models. -
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ChimeraDetector
ChimeraDetector detects aberrant chimeras in given genome sequences.
Chimeras are organisms composed of cells that originate from two or more different species. The name chimera comes from Greek mythology and describes a creature with the head of a lion, the body of a goat, the tail of a serpent and a head of dragon on its back. Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions to assess diversity or compare populations. Some randomly formed chimeras cause destruction. In plants... -
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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Automate everything: entity compliance, registered agent services, annual report and BOI filings, org charts, and DBA/fictitious name and business registration renewals, so you can focus on higher-value work.
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UMI-Reducer
collapsing technical duplicates via Unique Molecular Identifiers
Every sequencing library contains duplicate reads. While many duplicates arise during polymerase chain reaction (PCR), some of these duplicates derive from multiple identical fragments of mRNA present in the original lysate (termed "biological duplicates"). Unique Molecular Identifiers (UMIs) are random oligonucleotide sequences that allow differentiation between technical and biological duplicates. Here we report the development of UMI-Reducer, a new computational tool for processing... -
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cupSODA
Deterministic simulator of mass-action based models
cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action... -
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Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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pybrn is a Python package for the analysis of biochemical reaction networks. It provides basic model handling capabilities, import from SBML, analysis of conservation relations, steady state computation and model simulation.
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ChemStud
android app for engineers and scientists
Carryout unit conversions, perform definite integrals, solve for simultaneous equations and Ordinary Differential Equations from reaction data, solve for electrical engineering circuit problems and optimize linear programming problems -
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FAST Simulations
An Open source Analysis and SImulation Toolbox for Fuel Cells
... and developer, David B. Harvey. Features of FAST-fc include transport of gases and liquids, multi-step reaction kinetics, transient and steady state operation for performance and durability, and scalable dimensionality from 1D - 3D domains. Future development work is on-going in FAST-fc and our strategic development schedule includes membrane degradation, improved liquid water transport models through the application of pore networks, and extension to stack-level simulation. -
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ddtFoam
OpenFOAM solver to simulate the deflagration-to-detonation transition
This solver represents an addition to the open-source CFD package OpenFOAM. The solver is used to simulate the deflagration-to-detonation transition in hydrogen-air mixtures. Prominent features are described below. Additional description is available in the pdf file included. For a more detailed description download Florian Ettner's thesis (in German) from http://www.td.mw.tum.de/tum-td/de/forschung/dissertationen/download/I2013/Ettne13.pdf [8.6 MB] A shorter description (in... -
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PyWham
Python implementation of the Weighted Histogram Analysis Method (WHAM)
Latest version is 1.2, released Mar 12, 2016 PyWham is a flexible and fully customizable implementation of the Weighted Histogram Analysis Method (WHAM) in Python 2. PyWham has been carefully designed with flexibility in mind. Some of its features are: (1) any number of reaction coordinates, (2) any form of potential, (3) compatibility with Python syntax and Python math module and (4) support for user-defined functions. Knowledge of Python is not required. -
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LSDMap
Locally-Scaled Diffusion Maps from molecular dynamics trajectories
LSDMap is a set of Fortran90 codes parallelised with MPI for the calculation of Locally Scaled Diffusion Maps. The eigenvectors of the diffusion matrix can be used to form a small set of reaction coordinates describing the behaviour of a high-dimensional data set such as an equilibrium MD trajectory. -
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SPTEmu
A synchrophasotron emulator
A simulator for people who are interested in physics. Have you ever tried to calculate, e.g., nuclear reactions? I was totally confused by all these quants, neutrinos, alpha and beta decays, so I decided to create this synchrophasotron simulator. You just enter the reacting isotopes and/or particles and it simulates the reaction for you! P.S. It's called 'Synchrophasotron simulator' because I wanted the program to simulate particle colliding, but it doesn't do it yet. It just calculates alpha... -
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MLSTEZ is designed for next generation sequencing technology (PacBio CCS or Roche 454 platform) based MSLT methods. MLSTEZ, can automatically identify the barcodes and primers used in the PCR reaction, corrects sequencing errors, generates the MLST profile for each isolate, predicts the potential heterozygous locus, and outputs different alleles. Now ver2.0 supports asymmetric barcode design, please check manual for more details.
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fep1d
a script for the analysis of reaction coordinates
Fep1d is a script for the analysis of one-dimensional reaction coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (re-scale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, etc. -
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discremental
forever incremental hard disk based backups
This set of scripts is yet another rsync based backup solution. It uses the --link-dest option to create hard links to files that have not changed. Using this technique, each run results in a *full backup* even though the backup process used is incremental (only the files that changed since the last backup). This paradigm is sometimes called forever incremental backups. This utility exists because I wrote it a long time ago in reaction to the slow, cumbersome pace of the dirvish... -
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Cognitive Stability and Flexibility FIT
GPU Accelerated Fitting of Behavioral Data by a Physiological Model
... in the simulated paradigm and the activity of the rule 1 versus rule 2 representing population biases a decision module. The decision module implements a three dimensional nonlinear drift-diffusion process derived from a physiological winner-take-all network with four selective populations, representing the possible behavioral decisions. The decision module integrates top-down input from the rule module with bottom-up input from the decision module to produce decisions and reaction time distributions. -
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ThermV
Comprehensive thermal analysis software package
ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project... -
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RelKinema
Relativistic two-body kinematics calculator for nuclear reaction
Relativistic 2-body kinematics calculator for nuclear reaction, including mass data manager, result table browser and plotter. -
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simulate_pcr
PCR target prediction software
Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. This script predicts potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch tolerance and amplicon length range to be set by the user. The PCR amplicon simulation code also annotates... -
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ForStoch
Fortran Stochastic Simulator for Chemical Kinetics
ForStoch is a FORTRAN software suite for Stochastic Simulation of Checimal Kinetics. The stochastic simulation algorithm (SSA), proposed by Gillespie, is a cardinal simulation method for the chemical kinetics. Because the SSA simulates every reaction event, the amount of the computational time is huge when models have many reaction channels and species.This drawback motivates many attempts to improve the efficiency with the accuracy.The ForStoch includes orignial Gillespie SSA and other... -
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RSSA
Rejection-based stochastic simulation algorithm (RSSA)
Rejection-based stochastic simulation algorithm (RSSA) is an efficient exact algorithm for doing stochastic simulation of biochemical reaction systems. RSSA improves over state of the art of stochastic simulations by avoiding and collapsing as much the number of propensity updates. -
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Chemical Reaction
Balance chemical reaction and compute material balance
This Python program is used to balance a chemical reaction and to compute the material balance. Furthermore, it's able to check molecules and to write the condensed strutural formula from the name of an organic molecule. (Those both functionalities are still limited.) -
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modDFS
Find whether a KEGG module is complete in a proteome
Given module definitions and reaction information based on a KEGG database, modDFS does a depth first search to find whether a set of KOs are sufficient for completion of a module. For cases where only 1 absent KO would've been enough for module completion, that module is reported to be complete(only lenient). For cyclic modules, completion is defined as having all the module reaction steps present. Again, lenient completion cases are reported. Also, all absent reactions are reported so...